Starting phenix.real_space_refine
on Tue Feb  3 21:53:58 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9ucm_64048/02_2026/9ucm_64048.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ucm_64048/02_2026/9ucm_64048.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ucm_64048/02_2026/9ucm_64048.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ucm_64048/02_2026/9ucm_64048.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ucm_64048/02_2026/9ucm_64048.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ucm_64048/02_2026/9ucm_64048.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.066
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    4700      2.51       5
     N    1156      2.21       5
     O    1236      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7142
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3571
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 465, 3571
          Classifications: {'peptide': 465}
          Link IDs: {'PTRANS': 17, 'TRANS': 447}
          Chain breaks: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.01, per 1000 atoms: 0.28
  Number of scatterers: 7142
  At special positions: 0
  Unit cell: (84.7, 117.7, 94.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1236      8.00
     N    1156      7.00
     C    4700      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A  73 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  54 " - pdb=" SG  CYS B  73 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.61
  Conformation dependent library (CDL) restraints added in 271.1 milliseconds
  

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1660

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 0 sheets defined
      70.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 12
    Processing helix  chain 'A' and resid 16 through 19
    Processing helix  chain 'A' and resid 20 through 33
      removed outlier: 3.543A  pdb=" N   ILE A  25 " --> pdb=" O   PHE A  21 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   PHE A  30 " --> pdb=" O   LEU A  26 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   TYR A  33 " --> pdb=" O   THR A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 44
      removed outlier: 3.959A  pdb=" N   ILE A  43 " --> pdb=" O   ARG A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 69
      removed outlier: 3.549A  pdb=" N   ASN A  68 " --> pdb=" O   HIS A  65 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   ASP A  69 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 65 through 69'
    Processing helix  chain 'A' and resid 75 through 79
      removed outlier: 4.117A  pdb=" N   ASP A  79 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 101
      removed outlier: 3.520A  pdb=" N   VAL A  90 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASP A  91 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   PHE A  94 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LEU A  95 " --> pdb=" O   ASP A  91 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ALA A  97 " --> pdb=" O   ALA A  93 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.953A  pdb=" N   VAL A 107 " --> pdb=" O   PHE A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 138
      removed outlier: 3.748A  pdb=" N   MET A 122 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LEU A 123 " --> pdb=" O   SER A 119 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   THR A 129 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   PHE A 132 " --> pdb=" O   PHE A 128 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   GLY A 133 " --> pdb=" O   THR A 129 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   TYR A 136 " --> pdb=" O   PHE A 132 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   PHE A 137 " --> pdb=" O   GLY A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 157
      removed outlier: 4.044A  pdb=" N   PHE A 146 " --> pdb=" O   GLU A 142 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   VAL A 148 " --> pdb=" O   TRP A 144 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLN A 150 " --> pdb=" O   PHE A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 172
      removed outlier: 3.636A  pdb=" N   VAL A 165 " --> pdb=" O   TRP A 161 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   THR A 166 " --> pdb=" O   PRO A 162 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   TRP A 171 " --> pdb=" O   CYS A 167 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE A 172 " --> pdb=" O   VAL A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 185
    Processing helix  chain 'A' and resid 186 through 199
      removed outlier: 4.314A  pdb=" N   ASN A 192 " --> pdb=" O   THR A 188 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE A 198 " --> pdb=" O   LEU A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 210
    Processing helix  chain 'A' and resid 211 through 225
      removed outlier: 3.640A  pdb=" N   VAL A 223 " --> pdb=" O   ALA A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 292
      removed outlier: 3.928A  pdb=" N   LEU A 292 " --> pdb=" O   PHE A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 323
      removed outlier: 4.151A  pdb=" N   LEU A 302 " --> pdb=" O   VAL A 298 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   PHE A 306 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LEU A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   VAL A 310 " --> pdb=" O   PHE A 306 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   SER A 311 " --> pdb=" O   ALA A 307 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   LEU A 315 " --> pdb=" O   SER A 311 " (cutoff:3.500A)
      Proline residue:  A 319  - end of helix
      removed outlier: 3.542A  pdb=" N   ALA A 323 " --> pdb=" O   PRO A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 359
      removed outlier: 3.849A  pdb=" N   LEU A 339 " --> pdb=" O   ASP A 335 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ASP A 341 " --> pdb=" O   SER A 337 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY A 344 " --> pdb=" O   PHE A 340 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   ILE A 349 " --> pdb=" O   ILE A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 371
      removed outlier: 3.802A  pdb=" N   LEU A 369 " --> pdb=" O   CYS A 365 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU A 371 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 383
      removed outlier: 3.721A  pdb=" N   MET A 375 " --> pdb=" O   LEU A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 416
      Proline residue:  A 404  - end of helix
      removed outlier: 4.171A  pdb=" N   VAL A 412 " --> pdb=" O   ILE A 408 " (cutoff:3.500A)
      removed outlier: 5.142A  pdb=" N   SER A 413 " --> pdb=" O   THR A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 423
      removed outlier: 3.519A  pdb=" N   LEU A 422 " --> pdb=" O   HIS A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 451
      removed outlier: 3.788A  pdb=" N   ASP A 437 " --> pdb=" O   THR A 433 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ILE A 442 " --> pdb=" O   GLY A 438 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   GLY A 443 " --> pdb=" O   THR A 439 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ALA A 444 " --> pdb=" O   GLY A 440 " (cutoff:3.500A)
      Proline residue:  A 448  - end of helix
    Processing helix  chain 'A' and resid 454 through 458
    Processing helix  chain 'A' and resid 461 through 476
      removed outlier: 3.881A  pdb=" N   MET A 465 " --> pdb=" O   ASN A 461 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ILE A 467 " --> pdb=" O   PHE A 463 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   CYS A 474 " --> pdb=" O   ASP A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 493
      removed outlier: 3.654A  pdb=" N   TRP A 488 " --> pdb=" O   GLU A 484 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LYS A 489 " --> pdb=" O   ILE A 485 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   VAL A 490 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   SER A 491 " --> pdb=" O   ALA A 487 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 12
    Processing helix  chain 'B' and resid 16 through 19
    Processing helix  chain 'B' and resid 20 through 33
      removed outlier: 3.544A  pdb=" N   ILE B  25 " --> pdb=" O   PHE B  21 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   PHE B  30 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   TYR B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 44
      removed outlier: 3.958A  pdb=" N   ILE B  43 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 69
      removed outlier: 3.548A  pdb=" N   ASN B  68 " --> pdb=" O   HIS B  65 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   ASP B  69 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 65 through 69'
    Processing helix  chain 'B' and resid 75 through 79
      removed outlier: 4.118A  pdb=" N   ASP B  79 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 101
      removed outlier: 3.520A  pdb=" N   VAL B  90 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASP B  91 " --> pdb=" O   LEU B  87 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   PHE B  94 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LEU B  95 " --> pdb=" O   ASP B  91 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ALA B  97 " --> pdb=" O   ALA B  93 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA B  99 " --> pdb=" O   LEU B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 108
      removed outlier: 3.953A  pdb=" N   VAL B 107 " --> pdb=" O   PHE B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 138
      removed outlier: 3.748A  pdb=" N   MET B 122 " --> pdb=" O   LEU B 118 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LEU B 123 " --> pdb=" O   SER B 119 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   THR B 129 " --> pdb=" O   SER B 125 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   PHE B 132 " --> pdb=" O   PHE B 128 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   GLY B 133 " --> pdb=" O   THR B 129 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   TYR B 136 " --> pdb=" O   PHE B 132 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   PHE B 137 " --> pdb=" O   GLY B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 157
      removed outlier: 4.045A  pdb=" N   PHE B 146 " --> pdb=" O   GLU B 142 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   VAL B 148 " --> pdb=" O   TRP B 144 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLN B 150 " --> pdb=" O   PHE B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 172
      removed outlier: 3.637A  pdb=" N   VAL B 165 " --> pdb=" O   TRP B 161 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   THR B 166 " --> pdb=" O   PRO B 162 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   TRP B 171 " --> pdb=" O   CYS B 167 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   PHE B 172 " --> pdb=" O   VAL B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 185
    Processing helix  chain 'B' and resid 186 through 199
      removed outlier: 4.315A  pdb=" N   ASN B 192 " --> pdb=" O   THR B 188 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE B 198 " --> pdb=" O   LEU B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 210
    Processing helix  chain 'B' and resid 211 through 225
      removed outlier: 3.641A  pdb=" N   VAL B 223 " --> pdb=" O   ALA B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 292
      removed outlier: 3.928A  pdb=" N   LEU B 292 " --> pdb=" O   PHE B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 323
      removed outlier: 4.151A  pdb=" N   LEU B 302 " --> pdb=" O   VAL B 298 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   PHE B 306 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LEU B 309 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   VAL B 310 " --> pdb=" O   PHE B 306 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   SER B 311 " --> pdb=" O   ALA B 307 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   LEU B 315 " --> pdb=" O   SER B 311 " (cutoff:3.500A)
      Proline residue:  B 319  - end of helix
      removed outlier: 3.542A  pdb=" N   ALA B 323 " --> pdb=" O   PRO B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 359
      removed outlier: 3.850A  pdb=" N   LEU B 339 " --> pdb=" O   ASP B 335 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASP B 341 " --> pdb=" O   SER B 337 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY B 344 " --> pdb=" O   PHE B 340 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   ILE B 349 " --> pdb=" O   ILE B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 363 through 371
      removed outlier: 3.802A  pdb=" N   LEU B 369 " --> pdb=" O   CYS B 365 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU B 371 " --> pdb=" O   VAL B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 383
      removed outlier: 3.721A  pdb=" N   MET B 375 " --> pdb=" O   LEU B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 416
      Proline residue:  B 404  - end of helix
      removed outlier: 4.170A  pdb=" N   VAL B 412 " --> pdb=" O   ILE B 408 " (cutoff:3.500A)
      removed outlier: 5.141A  pdb=" N   SER B 413 " --> pdb=" O   THR B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 423
      removed outlier: 3.519A  pdb=" N   LEU B 422 " --> pdb=" O   HIS B 419 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 451
      removed outlier: 3.788A  pdb=" N   ASP B 437 " --> pdb=" O   THR B 433 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   ILE B 442 " --> pdb=" O   GLY B 438 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   GLY B 443 " --> pdb=" O   THR B 439 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ALA B 444 " --> pdb=" O   GLY B 440 " (cutoff:3.500A)
      Proline residue:  B 448  - end of helix
    Processing helix  chain 'B' and resid 454 through 458
    Processing helix  chain 'B' and resid 461 through 476
      removed outlier: 3.880A  pdb=" N   MET B 465 " --> pdb=" O   ASN B 461 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ILE B 467 " --> pdb=" O   PHE B 463 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   CYS B 474 " --> pdb=" O   ASP B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 493
      removed outlier: 3.654A  pdb=" N   TRP B 488 " --> pdb=" O   GLU B 484 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LYS B 489 " --> pdb=" O   ILE B 485 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   VAL B 490 " --> pdb=" O   LEU B 486 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   SER B 491 " --> pdb=" O   ALA B 487 " (cutoff:3.500A)

    320 hydrogen bonds defined for protein.
    912 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.01

  Time building geometry restraints manager: 0.77 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 2080
        1.34 -     1.46: 1607
        1.46 -     1.58: 3577
        1.58 -     1.70: 0
        1.70 -     1.82: 74
  Bond restraints: 7338
  Sorted by residual:
  bond pdb=" C   LYS A  41 "
       pdb=" N   PRO A  42 "
    ideal  model  delta    sigma   weight residual
    1.337  1.378 -0.041 9.80e-03 1.04e+04 1.78e+01
  bond pdb=" C   LYS B  41 "
       pdb=" N   PRO B  42 "
    ideal  model  delta    sigma   weight residual
    1.337  1.377 -0.040 9.80e-03 1.04e+04 1.68e+01
  bond pdb=" CG1 ILE A 149 "
       pdb=" CD1 ILE A 149 "
    ideal  model  delta    sigma   weight residual
    1.513  1.437  0.076 3.90e-02 6.57e+02 3.77e+00
  bond pdb=" CG1 ILE B 149 "
       pdb=" CD1 ILE B 149 "
    ideal  model  delta    sigma   weight residual
    1.513  1.438  0.075 3.90e-02 6.57e+02 3.71e+00
  bond pdb=" CB  VAL B 164 "
       pdb=" CG1 VAL B 164 "
    ideal  model  delta    sigma   weight residual
    1.521  1.462  0.059 3.30e-02 9.18e+02 3.24e+00
  ... (remaining 7333 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 9492
        2.16 -     4.32: 392
        4.32 -     6.48: 82
        6.48 -     8.64: 14
        8.64 -    10.80: 8
  Bond angle restraints: 9988
  Sorted by residual:
  angle pdb=" N   VAL B  46 "
        pdb=" CA  VAL B  46 "
        pdb=" C   VAL B  46 "
      ideal   model   delta    sigma   weight residual
     111.91  106.18    5.73 8.90e-01 1.26e+00 4.15e+01
  angle pdb=" N   VAL A  46 "
        pdb=" CA  VAL A  46 "
        pdb=" C   VAL A  46 "
      ideal   model   delta    sigma   weight residual
     111.91  106.18    5.73 8.90e-01 1.26e+00 4.15e+01
  angle pdb=" N   VAL A 471 "
        pdb=" CA  VAL A 471 "
        pdb=" C   VAL A 471 "
      ideal   model   delta    sigma   weight residual
     112.96  107.56    5.40 1.00e+00 1.00e+00 2.92e+01
  angle pdb=" N   VAL B 471 "
        pdb=" CA  VAL B 471 "
        pdb=" C   VAL B 471 "
      ideal   model   delta    sigma   weight residual
     112.96  107.58    5.38 1.00e+00 1.00e+00 2.90e+01
  angle pdb=" C   ARG A  40 "
        pdb=" N   LYS A  41 "
        pdb=" CA  LYS A  41 "
      ideal   model   delta    sigma   weight residual
     120.09  125.51   -5.42 1.25e+00 6.40e-01 1.88e+01
  ... (remaining 9983 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.04: 3919
       15.04 -    30.08: 201
       30.08 -    45.11: 38
       45.11 -    60.15: 6
       60.15 -    75.19: 4
  Dihedral angle restraints: 4168
    sinusoidal: 1546
      harmonic: 2622
  Sorted by residual:
  dihedral pdb=" CB  CYS A  54 "
           pdb=" SG  CYS A  54 "
           pdb=" SG  CYS A  73 "
           pdb=" CB  CYS A  73 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  150.79  -57.79     1      1.00e+01 1.00e-02 4.48e+01
  dihedral pdb=" CB  CYS B  54 "
           pdb=" SG  CYS B  54 "
           pdb=" SG  CYS B  73 "
           pdb=" CB  CYS B  73 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  150.75  -57.75     1      1.00e+01 1.00e-02 4.48e+01
  dihedral pdb=" CA  TRP A  75 "
           pdb=" C   TRP A  75 "
           pdb=" N   ALA A  76 "
           pdb=" CA  ALA A  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.88  -24.12     0      5.00e+00 4.00e-02 2.33e+01
  ... (remaining 4165 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 704
       0.047 -    0.094: 316
       0.094 -    0.141: 80
       0.141 -    0.188: 23
       0.188 -    0.235: 13
  Chirality restraints: 1136
  Sorted by residual:
  chirality pdb=" CA  THR A 410 "
            pdb=" N   THR A 410 "
            pdb=" C   THR A 410 "
            pdb=" CB  THR A 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.29    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  THR B 410 "
            pdb=" N   THR B 410 "
            pdb=" C   THR B 410 "
            pdb=" CB  THR B 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.29    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" CB  VAL B 168 "
            pdb=" CA  VAL B 168 "
            pdb=" CG1 VAL B 168 "
            pdb=" CG2 VAL B 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 1133 not shown)

  Planarity restraints: 1226
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  76 "    0.040 5.00e-02 4.00e+02   5.98e-02 5.73e+00
        pdb=" N   PRO A  77 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A  77 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A  77 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B  76 "   -0.040 5.00e-02 4.00e+02   5.97e-02 5.70e+00
        pdb=" N   PRO B  77 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO B  77 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B  77 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 161 "   -0.038 5.00e-02 4.00e+02   5.65e-02 5.11e+00
        pdb=" N   PRO A 162 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A 162 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 162 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1223 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2191
        2.83 -     3.35: 6472
        3.35 -     3.86: 10921
        3.86 -     4.38: 13029
        4.38 -     4.90: 22365
  Nonbonded interactions: 54978
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 119 "
            pdb=" O   GLY A 222 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" OG  SER B 119 "
            pdb=" O   GLY B 222 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" OG  SER B 125 "
            pdb=" NE2 GLN B 157 "
     model   vdw
     2.349 3.120
  nonbonded pdb=" OG  SER A 125 "
            pdb=" NE2 GLN A 157 "
     model   vdw
     2.349 3.120
  nonbonded pdb=" O   VAL A 354 "
            pdb=" OG1 THR A 358 "
     model   vdw
     2.370 3.040
  ... (remaining 54973 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.050
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.079   7340  Z= 0.339
  Angle     :  1.090  10.799   9992  Z= 0.602
  Chirality :  0.060   0.235   1136
  Planarity :  0.008   0.060   1226
  Dihedral  : 10.219  75.189   2502
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.73 (0.18), residues: 922
  helix: -3.81 (0.12), residues: 622
  sheet:  None (None), residues: 0
  loop : -3.29 (0.27), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 115 
 TYR   0.019   0.003   TYR A 136 
 PHE   0.019   0.002   PHE B  15 
 TRP   0.017   0.002   TRP A 138 
 HIS   0.017   0.003   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00809 ( 7338)
  covalent geometry    : angle       1.08971 ( 9988)
  SS BOND              : bond        0.00469 (    2)
  SS BOND              : angle       2.25932 (    4)
  hydrogen bonds       : bond        0.19535 (  320)
  hydrogen bonds       : angle       8.11003 (  912)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A   13 ARG cc_start: 0.8467 (tpp80) cc_final: 0.6857 (mmp-170)
REVERT: A   79 ASP cc_start: 0.7482 (p0) cc_final: 0.6850 (p0)
REVERT: A  415 ASP cc_start: 0.8196 (t0) cc_final: 0.7839 (t0)
REVERT: A  437 ASP cc_start: 0.8075 (t70) cc_final: 0.7779 (t0)
REVERT: B   13 ARG cc_start: 0.8144 (tpp80) cc_final: 0.6855 (mmp-170)
REVERT: B   47 LYS cc_start: 0.8154 (ttmm) cc_final: 0.7935 (tttp)
REVERT: B   79 ASP cc_start: 0.7635 (p0) cc_final: 0.7430 (p0)
REVERT: B  102 MET cc_start: 0.8895 (tpp) cc_final: 0.8678 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.0919
  time to fit residues: 19.2376
Evaluate side-chains
  103 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.0040
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.5992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.170020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.122055 restraints weight = 8489.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.17
r_work: 0.3156 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7340  Z= 0.122
  Angle     :  0.593   8.861   9992  Z= 0.303
  Chirality :  0.041   0.140   1136
  Planarity :  0.005   0.042   1226
  Dihedral  :  5.331  20.042    988
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  8.58 %
    Favored  : 89.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.15 (0.23), residues: 922
  helix: -2.57 (0.17), residues: 614
  sheet:  None (None), residues: 0
  loop : -2.76 (0.30), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  22 
 TYR   0.020   0.001   TYR A 316 
 PHE   0.009   0.001   PHE A 179 
 TRP   0.008   0.001   TRP B 184 
 HIS   0.004   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7338)
  covalent geometry    : angle       0.59333 ( 9988)
  SS BOND              : bond        0.00461 (    2)
  SS BOND              : angle       0.57521 (    4)
  hydrogen bonds       : bond        0.04353 (  320)
  hydrogen bonds       : angle       4.64901 (  912)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A   13 ARG cc_start: 0.8622 (tpp80) cc_final: 0.6781 (mmp-170)
REVERT: A   16 SER cc_start: 0.8453 (p) cc_final: 0.8222 (t)
REVERT: A   79 ASP cc_start: 0.7309 (p0) cc_final: 0.6880 (p0)
REVERT: A   91 ASP cc_start: 0.8412 (t0) cc_final: 0.7777 (m-30)
REVERT: A  449 LEU cc_start: 0.8439 (tt) cc_final: 0.8116 (tp)
REVERT: A  486 LEU cc_start: 0.6666 (tp) cc_final: 0.6425 (mt)
REVERT: B   13 ARG cc_start: 0.8335 (tpp80) cc_final: 0.6492 (mmp-170)
REVERT: B   47 LYS cc_start: 0.8176 (ttmm) cc_final: 0.7973 (tttp)
REVERT: B   91 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8116 (m-30)
REVERT: B  235 ASP cc_start: 0.8189 (m-30) cc_final: 0.7935 (m-30)
  outliers start: 14
  outliers final: 5
  residues processed: 115
  average time/residue: 0.0742
  time to fit residues: 11.8428
Evaluate side-chains
  102 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain A residue   73 CYS
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain B residue   73 CYS
Chi-restraints excluded: chain B residue   91 ASP
Chi-restraints excluded: chain B residue  480 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0010
   chunk 86 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0970
   chunk 44 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 52 optimal weight:   20.0000
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.4984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.172073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.124397 restraints weight = 8318.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.13
r_work: 0.3157 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3026 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7340  Z= 0.108
  Angle     :  0.571   9.877   9992  Z= 0.284
  Chirality :  0.041   0.155   1136
  Planarity :  0.004   0.035   1226
  Dihedral  :  4.793  17.796    988
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  :  9.50 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.20 (0.25), residues: 922
  helix: -1.88 (0.19), residues: 614
  sheet:  None (None), residues: 0
  loop : -2.30 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  22 
 TYR   0.017   0.001   TYR A 316 
 PHE   0.011   0.001   PHE B 179 
 TRP   0.006   0.001   TRP B 184 
 HIS   0.004   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 7338)
  covalent geometry    : angle       0.57085 ( 9988)
  SS BOND              : bond        0.00238 (    2)
  SS BOND              : angle       0.37352 (    4)
  hydrogen bonds       : bond        0.03690 (  320)
  hydrogen bonds       : angle       4.13999 (  912)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A   13 ARG cc_start: 0.8614 (tpp80) cc_final: 0.6714 (mmp-170)
REVERT: A   16 SER cc_start: 0.8402 (p) cc_final: 0.8201 (t)
REVERT: A   79 ASP cc_start: 0.7214 (p0) cc_final: 0.6825 (p0)
REVERT: A   91 ASP cc_start: 0.8345 (t0) cc_final: 0.7752 (m-30)
REVERT: A  449 LEU cc_start: 0.8421 (tt) cc_final: 0.8111 (tp)
REVERT: A  486 LEU cc_start: 0.6615 (tp) cc_final: 0.6393 (mt)
REVERT: B   13 ARG cc_start: 0.8345 (tpp80) cc_final: 0.6481 (mmp-170)
REVERT: B   79 ASP cc_start: 0.7245 (p0) cc_final: 0.6906 (p0)
REVERT: B   91 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.7824 (m-30)
REVERT: B  235 ASP cc_start: 0.8210 (m-30) cc_final: 0.7985 (m-30)
  outliers start: 15
  outliers final: 9
  residues processed: 109
  average time/residue: 0.0670
  time to fit residues: 10.0891
Evaluate side-chains
  101 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain A residue   73 CYS
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   73 CYS
Chi-restraints excluded: chain B residue   91 ASP
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  480 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 68 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 32 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN
A 141 HIS
B  68 ASN
B 141 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.169654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.121599 restraints weight = 8415.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.10
r_work: 0.3113 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7340  Z= 0.134
  Angle     :  0.572   7.661   9992  Z= 0.287
  Chirality :  0.042   0.145   1136
  Planarity :  0.004   0.035   1226
  Dihedral  :  4.633  16.812    988
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  :  9.37 %
    Favored  : 88.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.26), residues: 922
  helix: -1.42 (0.20), residues: 614
  sheet:  None (None), residues: 0
  loop : -1.90 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 293 
 TYR   0.016   0.001   TYR A 316 
 PHE   0.012   0.001   PHE B 179 
 TRP   0.007   0.001   TRP A 138 
 HIS   0.006   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7338)
  covalent geometry    : angle       0.57162 ( 9988)
  SS BOND              : bond        0.00214 (    2)
  SS BOND              : angle       0.42892 (    4)
  hydrogen bonds       : bond        0.03932 (  320)
  hydrogen bonds       : angle       4.01868 (  912)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A   13 ARG cc_start: 0.8619 (tpp80) cc_final: 0.6638 (mmp-170)
REVERT: A   79 ASP cc_start: 0.7205 (p0) cc_final: 0.6765 (p0)
REVERT: A   91 ASP cc_start: 0.8354 (t0) cc_final: 0.7928 (m-30)
REVERT: A  102 MET cc_start: 0.9012 (tpt) cc_final: 0.8504 (tpt)
REVERT: A  449 LEU cc_start: 0.8472 (tt) cc_final: 0.8130 (tp)
REVERT: A  486 LEU cc_start: 0.6732 (tp) cc_final: 0.6518 (mt)
REVERT: B   13 ARG cc_start: 0.8329 (tpp80) cc_final: 0.6290 (mmp-170)
REVERT: B   91 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.7827 (m-30)
REVERT: B  235 ASP cc_start: 0.8195 (m-30) cc_final: 0.7970 (m-30)
REVERT: B  437 ASP cc_start: 0.8205 (t70) cc_final: 0.8003 (t0)
REVERT: B  470 ASP cc_start: 0.7965 (t0) cc_final: 0.7746 (t0)
  outliers start: 18
  outliers final: 12
  residues processed: 100
  average time/residue: 0.0683
  time to fit residues: 9.5280
Evaluate side-chains
  100 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain A residue   73 CYS
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain B residue   16 SER
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   73 CYS
Chi-restraints excluded: chain B residue   91 ASP
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  480 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 83 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0070
   chunk 41 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.9404

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.168950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.120616 restraints weight = 8433.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.10
r_work: 0.3122 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7340  Z= 0.132
  Angle     :  0.557   6.986   9992  Z= 0.280
  Chirality :  0.042   0.145   1136
  Planarity :  0.004   0.036   1226
  Dihedral  :  4.492  15.319    988
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 10.29 %
    Favored  : 87.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.28 (0.27), residues: 922
  helix: -1.20 (0.20), residues: 622
  sheet:  None (None), residues: 0
  loop : -1.90 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 293 
 TYR   0.016   0.001   TYR A 117 
 PHE   0.013   0.001   PHE B 179 
 TRP   0.008   0.001   TRP A 138 
 HIS   0.006   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 7338)
  covalent geometry    : angle       0.55673 ( 9988)
  SS BOND              : bond        0.00174 (    2)
  SS BOND              : angle       0.44130 (    4)
  hydrogen bonds       : bond        0.03860 (  320)
  hydrogen bonds       : angle       3.96209 (  912)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A   13 ARG cc_start: 0.8674 (tpp80) cc_final: 0.6606 (mmp-170)
REVERT: A   79 ASP cc_start: 0.7228 (p0) cc_final: 0.6820 (p0)
REVERT: A   91 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.7778 (m-30)
REVERT: A  102 MET cc_start: 0.8969 (tpt) cc_final: 0.8492 (tpt)
REVERT: A  293 ARG cc_start: 0.8363 (mmt90) cc_final: 0.7985 (mmt90)
REVERT: A  449 LEU cc_start: 0.8566 (tt) cc_final: 0.8211 (tp)
REVERT: A  486 LEU cc_start: 0.6809 (tp) cc_final: 0.6579 (mt)
REVERT: B   13 ARG cc_start: 0.8455 (tpp80) cc_final: 0.6419 (mmp-170)
REVERT: B   75 TRP cc_start: 0.7658 (t-100) cc_final: 0.7326 (t-100)
REVERT: B   79 ASP cc_start: 0.7366 (p0) cc_final: 0.7008 (p0)
REVERT: B   91 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.7811 (m-30)
REVERT: B  235 ASP cc_start: 0.8242 (m-30) cc_final: 0.8029 (m-30)
REVERT: B  437 ASP cc_start: 0.8199 (t70) cc_final: 0.7990 (t0)
  outliers start: 19
  outliers final: 15
  residues processed: 105
  average time/residue: 0.0766
  time to fit residues: 11.2546
Evaluate side-chains
  109 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain A residue   73 CYS
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain B residue   16 SER
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   73 CYS
Chi-restraints excluded: chain B residue   91 ASP
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain B residue  480 LEU
Chi-restraints excluded: chain B residue  486 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 35 optimal weight:    0.1980
   chunk 58 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.172122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.123924 restraints weight = 8319.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.10
r_work: 0.3124 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7340  Z= 0.110
  Angle     :  0.532   5.655   9992  Z= 0.269
  Chirality :  0.041   0.146   1136
  Planarity :  0.004   0.036   1226
  Dihedral  :  4.333  14.669    988
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 11.87 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.97 (0.27), residues: 922
  helix: -0.95 (0.20), residues: 622
  sheet:  None (None), residues: 0
  loop : -1.80 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 293 
 TYR   0.014   0.001   TYR A 117 
 PHE   0.012   0.001   PHE B 179 
 TRP   0.009   0.001   TRP A  75 
 HIS   0.005   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 7338)
  covalent geometry    : angle       0.53187 ( 9988)
  SS BOND              : bond        0.00183 (    2)
  SS BOND              : angle       0.41515 (    4)
  hydrogen bonds       : bond        0.03552 (  320)
  hydrogen bonds       : angle       3.82883 (  912)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A   13 ARG cc_start: 0.8558 (tpp80) cc_final: 0.6444 (mmp-170)
REVERT: A   79 ASP cc_start: 0.7221 (p0) cc_final: 0.6830 (p0)
REVERT: A   91 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7570 (m-30)
REVERT: A  102 MET cc_start: 0.8956 (tpt) cc_final: 0.8555 (tpt)
REVERT: A  293 ARG cc_start: 0.8358 (mmt90) cc_final: 0.8004 (mmt90)
REVERT: A  449 LEU cc_start: 0.8539 (tt) cc_final: 0.8167 (tp)
REVERT: A  486 LEU cc_start: 0.6841 (tp) cc_final: 0.6630 (mt)
REVERT: B   13 ARG cc_start: 0.8446 (tpp80) cc_final: 0.6340 (mmp-170)
REVERT: B   79 ASP cc_start: 0.7389 (p0) cc_final: 0.6979 (p0)
REVERT: B   91 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7807 (m-30)
REVERT: B  235 ASP cc_start: 0.8242 (m-30) cc_final: 0.8036 (m-30)
  outliers start: 18
  outliers final: 12
  residues processed: 104
  average time/residue: 0.0809
  time to fit residues: 11.6885
Evaluate side-chains
  106 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain A residue   73 CYS
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   73 CYS
Chi-restraints excluded: chain B residue   91 ASP
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain B residue  486 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 29 optimal weight:    9.9990
   chunk 1 optimal weight:    0.6980
   chunk 6 optimal weight:    9.9990
   chunk 54 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.4980
   chunk 63 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.173935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.120874 restraints weight = 8216.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.53
r_work: 0.3144 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.2904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7340  Z= 0.133
  Angle     :  0.552   5.640   9992  Z= 0.278
  Chirality :  0.042   0.144   1136
  Planarity :  0.004   0.036   1226
  Dihedral  :  4.352  15.240    988
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 12.40 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.97 (0.27), residues: 922
  helix: -0.92 (0.20), residues: 626
  sheet:  None (None), residues: 0
  loop : -1.90 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 293 
 TYR   0.016   0.001   TYR A 117 
 PHE   0.012   0.001   PHE B 179 
 TRP   0.008   0.001   TRP A 138 
 HIS   0.006   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 7338)
  covalent geometry    : angle       0.55223 ( 9988)
  SS BOND              : bond        0.00191 (    2)
  SS BOND              : angle       0.49128 (    4)
  hydrogen bonds       : bond        0.03868 (  320)
  hydrogen bonds       : angle       3.87663 (  912)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A   13 ARG cc_start: 0.8448 (tpp80) cc_final: 0.6404 (mmp-170)
REVERT: A   79 ASP cc_start: 0.7194 (p0) cc_final: 0.6547 (p0)
REVERT: A   91 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7347 (m-30)
REVERT: A  102 MET cc_start: 0.8907 (tpt) cc_final: 0.8409 (tpt)
REVERT: A  293 ARG cc_start: 0.8348 (mmt90) cc_final: 0.7994 (mmt90)
REVERT: A  449 LEU cc_start: 0.8430 (tt) cc_final: 0.8045 (tp)
REVERT: A  486 LEU cc_start: 0.6801 (tp) cc_final: 0.6580 (mt)
REVERT: B   13 ARG cc_start: 0.8436 (tpp80) cc_final: 0.6462 (mmp-170)
REVERT: B   79 ASP cc_start: 0.7313 (p0) cc_final: 0.6830 (p0)
REVERT: B   91 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7582 (m-30)
  outliers start: 19
  outliers final: 14
  residues processed: 106
  average time/residue: 0.0674
  time to fit residues: 9.9919
Evaluate side-chains
  109 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   73 CYS
Chi-restraints excluded: chain B residue   91 ASP
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain B residue  480 LEU
Chi-restraints excluded: chain B residue  486 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 90 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 243 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.171716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.120221 restraints weight = 8337.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.43
r_work: 0.3137 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7340  Z= 0.167
  Angle     :  0.608   8.775   9992  Z= 0.304
  Chirality :  0.044   0.173   1136
  Planarity :  0.004   0.036   1226
  Dihedral  :  4.576  25.645    988
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 13.06 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.94 (0.27), residues: 922
  helix: -0.94 (0.20), residues: 614
  sheet:  None (None), residues: 0
  loop : -1.73 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 293 
 TYR   0.018   0.002   TYR A 117 
 PHE   0.011   0.001   PHE A  12 
 TRP   0.011   0.001   TRP A  75 
 HIS   0.007   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 7338)
  covalent geometry    : angle       0.60069 ( 9988)
  SS BOND              : bond        0.00161 (    2)
  SS BOND              : angle       4.76927 (    4)
  hydrogen bonds       : bond        0.04232 (  320)
  hydrogen bonds       : angle       3.99716 (  912)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A   13 ARG cc_start: 0.8448 (tpp80) cc_final: 0.6401 (mmp-170)
REVERT: A   79 ASP cc_start: 0.7368 (p0) cc_final: 0.6728 (p0)
REVERT: A   91 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7515 (m-30)
REVERT: A  293 ARG cc_start: 0.8349 (mmt90) cc_final: 0.8007 (mmt90)
REVERT: A  449 LEU cc_start: 0.8421 (tt) cc_final: 0.8030 (tp)
REVERT: A  486 LEU cc_start: 0.6973 (tp) cc_final: 0.6736 (mt)
REVERT: B   13 ARG cc_start: 0.8429 (tpp80) cc_final: 0.6450 (mmp-170)
REVERT: B   79 ASP cc_start: 0.7417 (p0) cc_final: 0.6882 (p0)
REVERT: B   91 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7633 (m-30)
  outliers start: 21
  outliers final: 15
  residues processed: 102
  average time/residue: 0.0867
  time to fit residues: 11.9548
Evaluate side-chains
  108 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain B residue   16 SER
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   73 CYS
Chi-restraints excluded: chain B residue   91 ASP
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  409 THR
Chi-restraints excluded: chain B residue  480 LEU
Chi-restraints excluded: chain B residue  486 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 69 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0670
   chunk 47 optimal weight:    0.1980
   chunk 89 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   chunk 91 optimal weight:    0.2980
   overall best weight:    0.3518

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.175825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.124875 restraints weight = 8223.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.43
r_work: 0.3220 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.3144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7340  Z= 0.096
  Angle     :  0.529   7.079   9992  Z= 0.268
  Chirality :  0.040   0.146   1136
  Planarity :  0.004   0.036   1226
  Dihedral  :  4.291  23.280    988
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 13.46 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.50 (0.28), residues: 922
  helix: -0.51 (0.21), residues: 618
  sheet:  None (None), residues: 0
  loop : -1.81 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 293 
 TYR   0.013   0.001   TYR A 117 
 PHE   0.013   0.001   PHE B 179 
 TRP   0.009   0.001   TRP B 184 
 HIS   0.004   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 ( 7338)
  covalent geometry    : angle       0.52383 ( 9988)
  SS BOND              : bond        0.00212 (    2)
  SS BOND              : angle       3.88031 (    4)
  hydrogen bonds       : bond        0.03194 (  320)
  hydrogen bonds       : angle       3.73502 (  912)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 ARG cc_start: 0.8449 (tpp80) cc_final: 0.6404 (mmp-170)
REVERT: A   79 ASP cc_start: 0.7377 (p0) cc_final: 0.6915 (p0)
REVERT: A   91 ASP cc_start: 0.7868 (t0) cc_final: 0.7176 (m-30)
REVERT: A  102 MET cc_start: 0.8912 (tpt) cc_final: 0.8515 (tpt)
REVERT: A  293 ARG cc_start: 0.8338 (mmt90) cc_final: 0.7998 (mmt90)
REVERT: A  449 LEU cc_start: 0.8377 (tt) cc_final: 0.7988 (tp)
REVERT: A  486 LEU cc_start: 0.6725 (tp) cc_final: 0.6504 (mt)
REVERT: B   13 ARG cc_start: 0.8392 (tpp80) cc_final: 0.6420 (mmp-170)
REVERT: B   79 ASP cc_start: 0.7315 (p0) cc_final: 0.6842 (p0)
REVERT: B   91 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7415 (m-30)
REVERT: B  293 ARG cc_start: 0.8387 (mmt90) cc_final: 0.8151 (mmt90)
REVERT: B  317 TRP cc_start: 0.7188 (t60) cc_final: 0.6968 (t60)
  outliers start: 16
  outliers final: 12
  residues processed: 110
  average time/residue: 0.0831
  time to fit residues: 12.5444
Evaluate side-chains
  110 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   73 CYS
Chi-restraints excluded: chain B residue   91 ASP
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  480 LEU
Chi-restraints excluded: chain B residue  486 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0980
   chunk 84 optimal weight:    0.3980
   chunk 38 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0470
   chunk 79 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 70 optimal weight:    8.9990
   chunk 17 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.7080

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.175072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.121957 restraints weight = 8215.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 2.51
r_work: 0.3162 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7340  Z= 0.115
  Angle     :  0.547   7.119   9992  Z= 0.277
  Chirality :  0.041   0.145   1136
  Planarity :  0.004   0.036   1226
  Dihedral  :  4.288  23.265    988
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 14.25 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.27), residues: 922
  helix: -0.51 (0.21), residues: 622
  sheet:  None (None), residues: 0
  loop : -1.89 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 293 
 TYR   0.014   0.001   TYR A 117 
 PHE   0.013   0.001   PHE B 179 
 TRP   0.012   0.001   TRP A  75 
 HIS   0.006   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7338)
  covalent geometry    : angle       0.54340 ( 9988)
  SS BOND              : bond        0.00182 (    2)
  SS BOND              : angle       3.19692 (    4)
  hydrogen bonds       : bond        0.03551 (  320)
  hydrogen bonds       : angle       3.74279 (  912)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 ARG cc_start: 0.8458 (tpp80) cc_final: 0.6382 (mmp-170)
REVERT: A   79 ASP cc_start: 0.7170 (p0) cc_final: 0.6545 (p0)
REVERT: A   91 ASP cc_start: 0.7871 (t0) cc_final: 0.7190 (m-30)
REVERT: A  102 MET cc_start: 0.8928 (tpt) cc_final: 0.8382 (tpt)
REVERT: A  293 ARG cc_start: 0.8330 (mmt90) cc_final: 0.7982 (mmt90)
REVERT: A  449 LEU cc_start: 0.8456 (tt) cc_final: 0.8097 (tp)
REVERT: A  486 LEU cc_start: 0.6798 (tp) cc_final: 0.6566 (mt)
REVERT: B   13 ARG cc_start: 0.8381 (tpp80) cc_final: 0.6386 (mmp-170)
REVERT: B   79 ASP cc_start: 0.7321 (p0) cc_final: 0.6816 (p0)
REVERT: B   91 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7406 (m-30)
REVERT: B  102 MET cc_start: 0.8996 (tpt) cc_final: 0.8576 (tpt)
REVERT: B  293 ARG cc_start: 0.8403 (mmt90) cc_final: 0.8161 (mmt90)
REVERT: B  449 LEU cc_start: 0.8467 (tt) cc_final: 0.8097 (tp)
  outliers start: 14
  outliers final: 12
  residues processed: 105
  average time/residue: 0.0803
  time to fit residues: 11.7869
Evaluate side-chains
  110 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   73 CYS
Chi-restraints excluded: chain B residue   91 ASP
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  480 LEU
Chi-restraints excluded: chain B residue  486 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 70 optimal weight:   20.0000
   chunk 4 optimal weight:    0.0980
   chunk 84 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0980
   chunk 24 optimal weight:    0.2980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.4780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.175253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.123727 restraints weight = 8280.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.44
r_work: 0.3188 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.3265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7340  Z= 0.102
  Angle     :  0.534   6.828   9992  Z= 0.273
  Chirality :  0.040   0.147   1136
  Planarity :  0.003   0.036   1226
  Dihedral  :  4.193  21.798    988
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.25 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.27 (0.28), residues: 922
  helix: -0.33 (0.21), residues: 618
  sheet:  None (None), residues: 0
  loop : -1.73 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 293 
 TYR   0.013   0.001   TYR A 117 
 PHE   0.013   0.001   PHE B 179 
 TRP   0.009   0.001   TRP A  75 
 HIS   0.005   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 7338)
  covalent geometry    : angle       0.53063 ( 9988)
  SS BOND              : bond        0.00152 (    2)
  SS BOND              : angle       2.96351 (    4)
  hydrogen bonds       : bond        0.03241 (  320)
  hydrogen bonds       : angle       3.68099 (  912)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1748.59 seconds
wall clock time: 30 minutes 35.56 seconds (1835.56 seconds total)